LaraFuhrmann
LaraFuhrmann
Consider the following [BAM-file](https://github.com/samtools/bcftools/files/6305196/deletion_issue.bam.gz) with [reference](https://github.com/samtools/bcftools/files/6305202/NC_045512.2.fasta.txt) and generate a consensus sequence using the following commands with bcftools version 1.12: ``` bcftools mpileup \ --max-depth 1000000 \ --max-idepth 100000 \ --annotate...
Fix of computation of popualtion_nucleotide_diversity.
When defining `datadir` different from `samples/` in the `config.yaml`, e.g. ``` input: reference: ../../resources/reference/ancestor_consensus.fasta datadir: ../../resources/samples/Experiment3 ``` the function `len_cutoff()` in `quality_assurance.smk` is taking the wrong part of the splitted...
I added config files and references for poliovirus and drosophila c virus. A short description with accession numbers for samples use is in the top of the config-files. Let me...
Hi :), I am using jax.numpy to define a NumPyro model. To do so it would be very useful to have a function doing essentially the same as numpy's put_along_axis....
Add the tool VILOCA to bioconda. ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates...
Added Benchmark study for VILOCA to the benchmarking.
For the revisions of the VILOCA manuscript, we had to extend the benchmarking study, - added a new simulation scenario - added two new methods - new figure